[DOC] display all masker reports in the doc #4295

Remi-Gau · 2024-02-28T17:40:30Z

Closes Render masker report as part of the documentation #4290

Changes proposed in this pull request:

example of maskers report are generated on every full build of the doc
they are viewable in the maskers section of the API part of the doc
add a notebook to help check the look of reports in notebooks

github-actions · 2024-02-28T17:40:43Z

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codecov · 2024-02-28T17:50:57Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.04%. Comparing base (abb80ff) to head (2dd5211).
Report is 21 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4295      +/-   ##
==========================================
+ Coverage   91.85%   92.04%   +0.19%     
==========================================
  Files         144      143       -1     
  Lines       16419    16438      +19     
  Branches     3434     3444      +10     
==========================================
+ Hits        15082    15131      +49     
+ Misses        792      764      -28     
+ Partials      545      543       -2

Flag	Coverage Δ
macos-latest_3.10_test_plotting	`91.92% <100.00%> (?)`
macos-latest_3.11_test_plotting	`91.92% <100.00%> (+0.06%)`	⬆️
macos-latest_3.8_test_plotting	`91.88% <100.00%> (?)`
macos-latest_3.9_test_plotting	`91.88% <100.00%> (?)`
ubuntu-latest_3.10_test_plotting	`91.92% <100.00%> (+0.06%)`	⬆️
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ubuntu-latest_3.12_test_pre	`91.92% <100.00%> (?)`
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ubuntu-latest_3.8_test_plotting	`91.88% <100.00%> (?)`
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windows-latest_3.10_test_plotting	`91.89% <100.00%> (?)`
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Remi-Gau · 2024-02-29T18:30:01Z

To view the masker reports as part of the doc but not "fixed":

https://output.circle-artifacts.com/output/job/d928521d-aa2b-41c2-8e44-cfaf3f0cfff3/artifacts/0/dev/modules/generated_reports/masker_reports_examples.html

Remi-Gau · 2024-02-29T18:34:30Z

doc/modules/generated_reports/masker_reports_examples.rst

+.. raw:: html
+   :file: nifti_masker.html


mention for each where they were taken from

Remi-Gau · 2024-02-29T20:00:25Z

Random thoughts from working on this.

we need to find a way to lint and format the HTML and CSS. The diffs become unmanageable otherwise.
a lot of the CSS should be refactored across reports (glm and maskers) to ensure a common style
some html sections should be also refactored across reports (for glm and maskers reports the footer section for example)

doc/visual_testing/reporter_visual_inspection_suite.py

Remi-Gau · 2024-03-01T13:27:39Z

Will try to extract a few things from this into separate PR to make it easier to review.

bthirion · 2024-03-03T22:09:19Z

Starts to look pretty good !

Remi-Gau · 2024-03-04T14:07:35Z

I would say that the run time optimization mentioned in this issue should be tackled in another PR.

bthirion

LGTM otherwise.

bthirion · 2024-03-04T21:10:17Z

doc/visual_testing/visualize_reports_in_notebook.ipynb

@@ -0,0 +1,212 @@
+{


I'm striggling to see where the resulting notebook can be found.

Sorry.

I put the notebook with the figures on a different branch. Because I don't think we want to commit that 9 MB monster to the repo.

Also it seems that the HTML report embedded are not viewable on github so it needs to be downloaded.

Clearly not optimal for an easy review.

https://github.com/Remi-Gau/nilearn/blob/notebooks/doc/visual_testing/visualize_reports_in_notebook.ipynb

It would be great to see them once ;-)

bthirion · 2024-03-04T21:40:52Z

The other issues is the set of failures. I guess it is unrelated.

Remi-Gau · 2024-03-05T09:39:49Z

Zipped HTMLified notebook is here:

visualize_reports_in_notebook.zip

bthirion

LGTM, thx.

Remi-Gau · 2024-03-05T21:21:07Z

will fix the doc build and merge if CI is still happy

* display masker reports in doc * update changelog * refactor * add notebooks * clear cells * [full doc] request full build * add link to examples * [full doc] request full build * fix doc build

…ap with masker report images (#4308) * extract table folding and overlapping * update changelog * Update doc/changes/latest.rst Co-authored-by: bthirion <bertrand.thirion@inria.fr> * FIX] fixes several plotting details in glm reports (#4266) * fix several issues in glm reports * further fixes * change cmap for glass brain * fix remaining issues * [full doc] request full build * update changelog * [full doc] request full build * [FIX] force views in surface plotting to be pairs of `int` or `float` when not a `string` (#4297) * for views to be pairs of int or float when not a string * update changelog * [FIX] fix cut position in nifti maps maskers (#4304) * fix cut position in nifti maps maskers * update changelog * [FIX] remove conftest for externals (#4306) * remove conftest tempita * ignore tempita in pyproject.toml * [MAINT] add script to check duration of test suite (#4231) * add script to check duration of test suite * add comment * comment and refactor * typo * improve paging * add workflow * Update maint_tools/requirements.txt * fail on bad request * upload artefacts * upload artefacts * remove running on PR * Apply suggestions from code review Co-authored-by: Elizabeth DuPre <emd222@cornell.edu> * update doc string * update doc string * refactor --------- Co-authored-by: Elizabeth DuPre <emd222@cornell.edu> * [DOC] display all masker reports in the doc (#4295) * display masker reports in doc * update changelog * refactor * add notebooks * clear cells * [full doc] request full build * add link to examples * [full doc] request full build * fix doc build * [full doc] request full build * [full doc] request full build --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: Elizabeth DuPre <emd222@cornell.edu>

…4310) * fix display of mutli maps masker * update changelog * Update doc/changes/latest.rst Co-authored-by: bthirion <bertrand.thirion@inria.fr> * [DOC] display all masker reports in the doc (#4295) * display masker reports in doc * update changelog * refactor * add notebooks * clear cells * [full doc] request full build * add link to examples * [full doc] request full build * fix doc build * [full doc] request full build * [full doc] request full build --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr>

Remi-Gau changed the title ~~[FIX] update layout of maskers report to avoid overlap between sections~~ [FIX] update layout of maskers reports Feb 29, 2024

Remi-Gau commented Feb 29, 2024

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bthirion reviewed Feb 29, 2024

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Remi-Gau mentioned this pull request Mar 1, 2024

[MAINT] Use prettier to format HTML and CSS #4302

Merged

This was referenced Mar 4, 2024

[ENH] add footer to all reports #4307

Draft

Standardize footer of reports #4300

Open

[FIX] make masker report tables horizontally scrollable and not overlap with masker report images #4308

Merged

display masker reports in doc

4783071

Remi-Gau force-pushed the fix/4281 branch from 389c4f9 to 4783071 Compare March 4, 2024 09:33

Remi-Gau changed the title ~~[FIX] update layout of maskers reports~~ [DOC] display all masker reports in the doc Mar 4, 2024

update changelog

b2f37a7

Remi-Gau marked this pull request as ready for review March 4, 2024 10:00

Remi-Gau marked this pull request as draft March 4, 2024 10:01

Remi-Gau added 3 commits March 4, 2024 11:27

Merge remote-tracking branch 'upstream/main' into fix/4281

30d56f4

refactor

6dd96d5

add notebooks

3731e90

Remi-Gau marked this pull request as ready for review March 4, 2024 14:03

clear cells

24a2931

Remi-Gau requested a review from bthirion March 4, 2024 14:10

[full doc] request full build

11c8c39

bthirion reviewed Mar 4, 2024

View reviewed changes

add link to examples

55d5525

Remi-Gau added 2 commits March 5, 2024 09:37

Merge remote-tracking branch 'upstream/main' into fix/4281

d1daf37

[full doc] request full build

92375d8

bthirion approved these changes Mar 5, 2024

View reviewed changes

Remi-Gau mentioned this pull request Mar 5, 2024

[FIX] use the proper html template for mutli maps and label masker #4310

Merged

fix doc build

2dd5211

Remi-Gau merged commit c43d5f9 into nilearn:main Mar 5, 2024
32 of 33 checks passed

Remi-Gau deleted the fix/4281 branch March 5, 2024 22:34

Remi-Gau mentioned this pull request Apr 9, 2024

report CSS and code refactor #4368

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[DOC] display all masker reports in the doc #4295

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[DOC] display all masker reports in the doc #4295

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